v0.1.1

This release fixes a bug in v0.1.0 where support for non-destructive events (DUP and INV) might not be appropriately counted. It is also slightly more specific about including soft-clipped read support which may reduce support relative to v0.1.0 in some cases.

v0.1.0

• No longer requires MC (mate CIGAR) or MQ (mate mapping quality) tags from Samblaster
• No longer require splitters.bam file from Samblaster. All split-reads are filtered internally using the BWA-MEM SA tag
• Can read (and write) library information as a JSON file using the -l flag
• Can output a sparse BAM file of the reads used for genotyping with the -w flag (for diagnostic purposes).
• Much more memory efficient
• ~50% faster than v0.0.4
• Can read CRAM files as input
• Now assesses clipped reads (in addition to split reads) to call breakpoint genotypes

Many thanks to @ernfrid for help with development, testing, and benchmarking for this release

v0.0.4

Bug fix for https://github.com/hall-lab/svtyper/releases/tag/v0.0.3 for a serious bug introduced in 9dd73d2 that caused SVTyper to ignore paired-end evidence. Patched with a2a9381 (which is included in this release

v0.0.3

EDIT: Do not use this version, as it includes a serious bug introduced in 9dd73d2 that causes SVTyper to ignore paired-end evidence. Patched in a2a9381

Minor update

• splitters.bam can be omitted (but this will not consider split-read evidence
• for deletions smaller than 2 x stdev of library insert, ignore paired-end evidence, due to low power
• speed improvement (~25%, thanks to @brentp )
• Set GQ to integer (in accordance with VCF spec)
• ignore libraries that constitute < 0.1% of BAM file

v0.0.2

• no longer assumes non-reference genotype. Can be used to naively genotype variants that may be homozygous reference
• generates empirical histogram of insert sizes
• examines both sides of INV (inversion) variants
• better overflow/underflow protection